## ## SIEMENSPRISMAFIT SIEMENSTIMTRIO SIEMENSVERIO ## 58 1185 36
## ## CHP HSC PNC ## 36 58 1185
12/18/2020
## ## SIEMENSPRISMAFIT SIEMENSTIMTRIO SIEMENSVERIO ## 58 1185 36
## ## CHP HSC PNC ## 36 58 1185
## ## CHP HSC PNC ## SIEMENSPRISMAFIT 0 58 0 ## SIEMENSTIMTRIO 0 0 1185 ## SIEMENSVERIO 36 0 0
Excluding HSC-SIEMENSTIMTRIO (n=7) for now.
## [1] "Batches:"
## [1] "CHP-SIEMENSVERIO" "HSC-SIEMENSPRISMAFIT" "PNC-SIEMENSTIMTRIO"
## Analysis of Variance Table ## ## Response: age ## Df Sum Sq Mean Sq F value Pr(>F) ## site 2 1012.5 506.27 34.606 2.313e-15 *** ## Residuals 1276 18667.2 14.63 ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Age is confounded across sites.
## ## FEMALE MALE ## CHP 24 12 ## HSC 37 21 ## PNC 630 555
## ## FEMALE MALE ## CHP 0.6666667 0.3333333 ## HSC 0.6379310 0.3620690 ## PNC 0.5316456 0.4683544
## ## Pearson's Chi-squared test ## ## data: df$site and df$sex ## X-squared = 4.8976, df = 2, p-value = 0.0864
Visualization and harmonization of intracraneal volumes (ICV)
Visualization and harmonization of 145 volumes
ICV normalization and visualization
Harmonization of intracraneal volume (ICV).
A. As single dataset.
B. By Splitting data by Males and Females (M/F).
Harmonization of 145 volumes
A. As single dataset.
B. By splitting data by Males and Females (M/F).
C. By splitting data by tissues (Tissue).
D. B + C.
ICV Normalization of 145 volumes
A. No adjustment.
B. ICV Residualization: Splitting data by Males and Females (M/F).
C. ICV Residualization: Joint (i.e. no M/F split).
D. ICV as Covariate.
| ICV | ICV [M] | ICV [F] | |
|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates |
| (Intercept) | -0.50 *** | -0.00 | 0.00 |
| age | 0.03 | 0.12 ** | -0.05 |
| sex [MALE] | 1.08 *** | ||
| age2 | -0.05 * | -0.05 | -0.07 |
| Observations | 1185 | 555 | 630 |
| R2 / R2 adjusted | 0.290 / 0.288 | 0.017 / 0.013 | 0.006 / 0.003 |
|
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| ICV [M] | |||
|---|---|---|---|
| Predictors | Estimates | CI | p |
| (Intercept) | -0.00 | -0.08 – 0.08 | 1.000 |
| age | 0.12 | 0.03 – 0.20 | 0.005 |
| Observations | 555 | ||
| R2 / R2 adjusted | 0.014 / 0.012 | ||
| ICV [F] | |||
|---|---|---|---|
| Predictors | Estimates | CI | p |
| (Intercept) | 0.00 | -0.08 – 0.08 | 1.000 |
| age | -0.04 | -0.12 – 0.04 | 0.348 |
| Observations | 630 | ||
| R2 / R2 adjusted | 0.001 / -0.000 | ||
| ICV | |||
|---|---|---|---|
| Predictors | Estimates | CI | p |
| (Intercept) | 0.00 | -0.06 – 0.06 | 1.000 |
| age | -0.01 | -0.07 – 0.04 | 0.635 |
| Observations | 1185 | ||
| R2 / R2 adjusted | 0.000 / -0.001 | ||
## Analysis of Variance Table ## ## Model 1: X702 ~ sex + age + age * sex ## Model 2: X702 ~ sex + age + age * sex + batch ## Res.Df RSS Df Sum of Sq F Pr(>F) ## 1 1275 1.9996e+13 ## 2 1273 1.9786e+13 2 2.099e+11 6.7524 0.00121 ** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Analysis of Variance Table ## ## Model 1: ICV ~ sex + age ## Model 2: ICV ~ sex + age + batch ## Res.Df RSS Df Sum of Sq F Pr(>F) ## 1 1276 1.9760e+13 ## 2 1274 1.9759e+13 2 753810856 0.0243 0.976
Past this point, all reference to ICV refers to ICV harmonized by splitting data by sex (M/F; Option 1B).
M/F lines up residualized WM volumes best.
M/F also performs the best on residualized GM volumes.
Past this point, all reference to ROI refers refers to ROIs harmonized by splitting data by sex (M/F; Option 2B).
For each of the 145 ROI volumes, two models were used:
- Model 1: ROI ~ sex + age + agexsex (+ ICV)
- Model 2: ROI ~ sex + age + agexsex (+ ICV) + batch
Number of models for which batch variables contributes new information is shown below.
## Raw Raw (ICV adj) Combat Combat (ICV adj) ## 36 43 0 0
ROIs are corrected for ICV with the formula
\[ROI_{adj} = ROI - \beta (ICV - \overline{ICV})\]
where \(\beta\) represents the ICV-ROI slope and \(\overline{ICV}\) is the average ICV of subjects in the cohort used for the correction.
In this presentation, two cohorts (i.e. males and females) are corrected separately. Effects of using only one cohort are also shown.
(Covariance) PCA was performed with (M/F) ICV-corrected volumes. Then GM and WM totals were projected onto PCs 1 and 2.
## contr ROI_INDEX ROI_NAME HEMISPHERE TISSUE_SEG ## 1 28.917845 81 frontal lobe WM right Right WM ## 2 28.259090 82 frontal lobe WM left Left WM ## 3 9.032425 87 temporal lobe WM right Right WM ## 4 8.372905 88 temporal lobe WM left Left WM ## 5 7.895716 86 parietal lobe WM left Left WM ## 6 7.033472 85 parietal lobe WM right Right WM
Note: Blue lines denote supplementary projections.
Sex differences are retained after ICV-residualizing by sex (M/F Residualization).
Alternatively, GM loses contr. toward Dim 2 and sex differences are eliminated if ICV is residualized irrespective of sex (i.e. Joint Residualization).
| WM | WM (M/F Res.) | WM (Joint Res.) | WM | |
|---|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates | Estimates |
| (Intercept) | -0.43 *** | -0.66 *** | 0.01 | -8.54 *** |
| age | 0.32 *** | 0.55 *** | 0.72 *** | 0.36 *** |
| sex [MALE] | 0.94 *** | 1.43 *** | -0.01 | -0.02 |
| age * sex [MALE] | 0.14 ** | 0.01 | 0.03 | 0.01 |
| ICV | 0.00 *** | |||
| Observations | 1279 | 1279 | 1279 | 1279 |
| R2 / R2 adjusted | 0.335 / 0.333 | 0.737 / 0.736 | 0.542 / 0.541 | 0.889 / 0.889 |
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In parentheses: ICV normalization method.
| WM | WM (M/F Res.) | WM (Joint Res.) | WM | |
|---|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates | Estimates |
| (Intercept) | 0.47 *** | 0.72 *** | -0.08 ** | -8.57 *** |
| age | 0.46 *** | 0.55 *** | 0.74 *** | 0.36 *** |
| age2 | -0.07 | -0.02 | -0.04 | -0.02 |
| ICV[M_filter] | 0.00 *** | |||
| Observations | 588 | 588 | 588 | 588 |
| R2 / R2 adjusted | 0.229 / 0.226 | 0.515 / 0.513 | 0.528 / 0.526 | 0.872 / 0.871 |
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| WM | WM (M/F Res.) | WM (Joint Res.) | WM | |
|---|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates | Estimates |
| (Intercept) | -0.40 *** | -0.61 *** | 0.07 ** | -8.49 *** |
| age | 0.33 *** | 0.55 *** | 0.73 *** | 0.36 *** |
| age2 | -0.10 ** | -0.06 *** | -0.08 *** | -0.04 ** |
| ICV[F_filter] | 0.00 *** | |||
| Observations | 691 | 691 | 691 | 691 |
| R2 / R2 adjusted | 0.157 / 0.154 | 0.557 / 0.555 | 0.557 / 0.556 | 0.859 / 0.859 |
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| GM | GM (M/F Res.) | GM (Joint Res.) | GM (Joint Cov.) | |
|---|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates | Estimates |
| (Intercept) | -0.47 *** | -0.68 *** | -0.07 * | -8.34 *** |
| age | -0.34 *** | -0.45 *** | -0.70 *** | -0.31 *** |
| sex [MALE] | 1.04 *** | 1.48 *** | 0.15 *** | 0.10 *** |
| age * sex [MALE] | 0.12 ** | -0.00 | -0.02 | -0.00 |
| ICV | 0.00 *** | |||
| Observations | 1279 | 1279 | 1279 | 1279 |
| R2 / R2 adjusted | 0.384 / 0.383 | 0.806 / 0.806 | 0.518 / 0.517 | 0.906 / 0.906 |
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| GM | GM (M/F Res.) | GM (Joint Res.) | GM (Joint Cov.) | |
|---|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates | Estimates |
| (Intercept) | 0.59 *** | 0.84 *** | 0.15 *** | -8.42 *** |
| age | -0.22 *** | -0.44 *** | -0.71 *** | -0.31 *** |
| age2 | -0.03 | 0.03 | 0.06 | 0.02 |
| ICV[M_filter] | 0.00 *** | |||
| Observations | 588 | 588 | 588 | 588 |
| R2 / R2 adjusted | 0.068 / 0.064 | 0.489 / 0.487 | 0.502 / 0.500 | 0.866 / 0.865 |
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| GM | GM (M/F Res.) | GM (Joint Res.) | GM (Joint Cov.) | |
|---|---|---|---|---|
| Predictors | Estimates | Estimates | Estimates | Estimates |
| (Intercept) | -0.50 *** | -0.72 *** | -0.13 *** | -8.24 *** |
| age | -0.35 *** | -0.45 *** | -0.71 *** | -0.32 *** |
| age2 | -0.02 | 0.06 *** | 0.10 *** | 0.04 *** |
| ICV[F_filter] | 0.00 *** | |||
| Observations | 691 | 691 | 691 | 691 |
| R2 / R2 adjusted | 0.177 / 0.175 | 0.532 / 0.530 | 0.526 / 0.524 | 0.871 / 0.870 |
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<Insert references for Combat and ICV-normalization.>